Biology subjects

Lin, Y.

Publications and source records attributed to Lin, Y..

At least 415 records · Page 23Linked to original sources

bioRxiv2019

Age-dependent sexual dimorphism in the adult human gut microbiota

A decade of studies has established the importance of the gut microbiome in human health. In spite of sex differences in the physiology, lifespan, and prevalence of many age-associated diseases, sex and age disparities in the gut microbiota have been little studied. Here we show age-related sex differences in the adult gut microbial composition and functionality in two community-based cohorts from Northern China and the Netherlands. Consistently, women harbour a more diverse and stable microbial community across broad age ranges, whereas men exhibit a more variable gut microbiota strongly correlated with age. Reflecting the sex-biased age-gut microbiota interaction patterns, sex differences observed in younger adults are considerably reduced in the elderly population. Our findings highlight the age- and sex-biased differences in the adult gut microbiota across two ethnic population and emphasize the need for considering age and sex in studies of the human gut microbiota.

genomics↗

bioRxiv2019

3D Multicolor Nanoscopy at 10,000 Cells a Day

Diffraction-unlimited single-molecule techniques like STORM and (F)PALM enable three-dimensional (3D) fluorescence imaging at tens of nanometer resolution and are invaluable to investigate sub-cellular organization. The multitude of camera frames required to reconstruct a super-resolved image limits the typical throughput of these techniques to tens of cells per day, rendering these methods incompatible with large-scale cell biological or clinical application. STORM acquisition rates can be increased by over an order of magnitude, however the data volumes of about 40 TB a day and concomitant analysis burdens exceed the capacity of existing workflows. Here we present an integrated platform which transforms SMLM from a trick-pony technique into a work horse for cell biology. We leverage our developments in microscopy-specific data compression, distributed storage, and distributed analysis to automatically perform real-time localization analysis, which enable SMLM at throughputs of 10,000 cells a day. We implemented these advances in a fully-integrated environment that supports a highly-flexible architecture for distributed analysis, enabling quickly- and graphically-reconfigurable analyses to be automatically initiated from the microscope during acquisition, remotely executed, and even feedback and queue new acquisition tasks on the microscope. We demonstrate the utility of this framework by imaging hundreds of cells per well in multi-well sample formats. Our platform, the PYthon-Microscopy Environment (PYME), is easily configurable for hardware control on custom microscopes, and includes a plugin framework so users can readily extend all components of their imaging, visualization, and analysis pipeline. PYME is cross-platform, open source, and efficiently puts high-caliber visualization and analysis tools into the hands of both microscope developers and users.

biophysics↗

bioRxiv2019

A multi-omic cohort as a reference point for promoting a healthy human gut microbiome

More than a decade of gut microbiome studies have a common goal for human health. As most of the disease studies sample the elderly or the middle-aged, a reference cohort for young individuals has been lacking. It is also not clear what other omics data need to be measured to better understand the gut microbiome. Here we present high-depth metagenomic shotgun sequencing data for the fecal microbiome together with other omics data in a cohort of 2,183 adults, and observe a number of vitamins, hormones, amino acids and trace elements to correlate with the gut microbiome and cluster with T cell receptors. Associations with physical fitness, sleeping habits and dairy consumption are identified in this large multi-omic cohort. Many of the associations are validated in an additional cohort of 1,404 individuals. Our comprehensive data are poised to advise future study designs to better understand and manage our gut microbiome both in population and in mechanistic investigations.

microbiology↗

bioRxiv2019

An Array of 60,000 Antibodies for Proteome-Scale Antibody Generation and Target Discovery

Antibodies are essential for elucidating the roles of genes decoded by genome sequencing. However, affordable technology for proteome-scale antibody generation does not exist. To address this, we developed the Proteome Epitope Tag Antibody Library (PETAL) and its array. PETAL consists of 62,208 mAbs against 15,199 peptides from diverse proteomes. PETAL harbors binders for a great multitude of proteins in nature due to antibody multispecificity, an intrinsic feature of an antibody. Distinctive combinations of 10,000-20,000 mAbs were found to target specific proteomes by array screening. Phenotype-specific mAb-target pairs were discovered for maize and zebrafish samples. Immunofluorescence and flow cytometry mAbs for human membrane proteins and ChIP-seq mAbs for transcription factors were identified from respective proteome-binding PETAL mAbs. Differential screening of cell surface proteomes of tumor and normal tissues discovered internalizing tumor antigens for antibody-drug conjugates. By discovering high affinity mAbs at a fraction of current time and cost, PETAL enables proteome-scale antibody generation and target discovery.

systems biology↗

bioRxiv2019

Insights into the mysterious genetic variation profile of tprK inTreponema pallidum under the development of natural human syphilis infection

Although the variations of the tprK gene in Treponema pallidum were considered to play a critical role in the pathogenesis of syphilis, how actual variable characteristics of tprK in the course of natural human infection enabling the pathogens survive has thus far remained unclear. Here, we performed NGS to investigate tprK of T. pallidum directly from primary and secondary syphilis samples. Compared with diversity in tprK of the strains from primary syphilis samples, there were more mixture variants found within seven V regions of the tprK gene among the strains from secondary syphilis samples, and the frequencies of predominant sequences within V regions of tprK were generally decreased (less than 80%) with the proportion of minor variants in 10-60% increasing. Noteworthy, the variations within V regions of tprK always obeyed a strict 3 bp changing pattern. And tprK in the strains from the two-stage samples kept some stable amino acid sequences within V regions. Particularly, the amino acid sequences IASDGGAIKH and IASEDGSAGNLKH in V1 not only presented a high proportion of inter-population sharing, but also presented a relatively high frequency (above 80%) in the populations. Besides, tprK always demonstrated remarkable variability in V6 at both the intra- and inter-strain levels regardless of the course. These findings unveiled that the different profile of tprK in T. pallidum directly from primary and secondary syphilis samples, indicating that throughout the development of syphilis T. pallidum constantly varies its domain tprK gene to obtain the best adaptation to the host. While this changing was always subjected a strict gene conversion mechanism to keep an abnormal TprK. The highly stable peptides found in V1 would probably be promising potential vaccine components. And the highly heterogenetic regions (e.g. V6) could provide insight into the mysterious role of tprK in immune evasion. Author summaryAlthough the variations of the tprK gene in Treponema pallidum were considered to play a critical role in the pathogenesis of syphilis, how actual variable characteristics of tprK in the course of natural human infection enabling the pathogens survive has thus far remained unclear. Here, we performed next-generation sequencing, a more sensitive and reliable approach, to investigate tprK of Treponema pallidum directly from primary and secondary syphilis patients, revealing that the profile of tprK in T. pallidum from the two-stage samples was different. Within the strains from secondary syphilis patients, more mixture variants within seven V regions of tprK were found, the frequencies of their predominant sequences were generally decreased with the proportion of minor variants in 10-60% was increased. And the variations within V regions of tprK always obeyed a strict 3 bp changing pattern. Noteworthy, the amino acid sequences IASDGGAIKH and IASEDGSAGNLKH in V1 presented a high proportion of inter-population sharing and presented a relatively high frequency in the populations. And V6 region always demonstrated remarkable variability at intra- and inter-patient levels regardless of the course. These findings provide insights into the mysterious role of TprK in immune evasion and for further exploring the potential vaccine components.

microbiology↗

bioRxiv2019

Moraxellaceae and Moraxella interact with the altered airway mycobiome in asthma

Airway microbial-microbial interaction plays an important role in chronic airway inflammatory diseases such as asthma. Moraxella is widely regarded as a human respiratory tract pathogen. We aimed to investigate the interactions among Moraxella, Moraxellaceae (to which Moraxella belongs) and the airway microbiome in asthma. Induced sputum samples were obtained from 116 asthma patients and 29 healthy individuals, and the bacterial/fungal communities were profiled using 16S rRNA and ITS1 DNA gene sequencing. We found that asthma patients harboured significantly greater airway bacterial and fungal -diversity than that of healthy individuals. Moraxellaceae, Moraxella and Moraxella otu19 (bacteria), and Schizophyllaceae, Polyporaceae, Aspergillus, Schizophyllum and Candida (fungi) were increased in the airway of asthma. Moreover, Moraxellaceae, Schizophyllaceae, Polyporaceae and Candida were positively associated with airway fungal -diversity. Correlation networks revealed Moraxellaceae and Moraxella as microbial \"hubs\" in asthma that had significant negative connections with multiple bacterial communities, such as Leptotrichiaceae, Lachnospiraceae, Peptostreptococcaceae, Porphyromonadaceae, Prevotella, Veillonella, Rothia and Leptotrichia, but positive interactions with fungal communities such as Schizophyllaceae, Polyporaceae, Candida and Meyerozyma. Together, our finding revealed an altered microbiome and complex microbial-microbial interactions in the airway of asthma. Moraxellaceae and Moraxella showed significant interactions with the airway mycobiome, providing potential insights into the novel pathogenic mechanisms of asthma.\n\nIMPORTANCEWith the advent of culture-independent techniques, growing evidence suggests that the airway microbiome is closely correlated with chronic respiratory diseases such as asthma. The complex microbial-microbial interaction exists in the airways of both healthy individuals and patients with respiratory diseases, which is of great significance for the pathogenesis and disease progression of asthma. In this study, we evaluated the airway dysbiosis in asthma patients, described the interaction between Moraxellaceae, Moraxella and airway bacterial/fungal communities, and it contributes to further understanding the pathogenic mechanisms of asthma.

microbiology↗

bioRxiv2018

Genome-wide association meta-analysis identifies novel GP2 gene risk variants for pancreatic cancer in the Japanese population

The etiology of pancreatic cancer remains largely unknown. Here, we report the results of a meta-analysis of three genome-wide association studies (GWASs) comprising 2,039 pancreatic cancer cases and 32,592 controls, the largest sample size in the Japanese population. We identified 3 (13q12.2, 13q22.1, and 16p12.3) genome-wide significant loci (P<5.0x10-8) and 4 suggestive loci (P<1.0x10-6) for pancreatic cancer. Of these risk loci, 16p12.3 is novel; the lead SNP maps to rs78193826 (odds ratio (OR)=1.46, 95% CI=1.29-1.66, P=4.28x10-9), an Asian-specific, nonsynonymous glycoprotein 2 (GP2) gene variant predicted to be highly deleterious. Additionally, the gene-based GWAS identified a novel gene, KRT8, which is linked to exocrine pancreatic and liver diseases. The identified GP2 gene variants were pleiotropic for multiple traits, including type 2 diabetes, hemoglobin A1c (HbA1c) levels, and pancreatic cancer. Mendelian randomization analyses corroborated causality between HbA1c and pancreatic cancer. These findings suggest that GP2 gene variants are associated with pancreatic cancer susceptibility in the Japanese population, prompting further functional characterization of this locus.

genetics↗

bioRxiv2018

Genomic analyses provide insights into genetic architecture of three-way crossbred pigs

BackgroundCrossbreeding is effective for improving performance in poultry and livestock, which is mainly attributed to heterosis. For pork production, a classic three-way crossbreeding system of Duroc x (Landrace x Yorkshire) (DLY) is widely used to produce terminal crossbred pigs with stable and prominent performance. Nonetheless, studies on the transmission of genetic information and gene expression pattern of DLY have been limited.\n\nFindingsWe analyzed population-scale SNPs based on 30 individuals from these three purebreds and identified 529.93 K SNPs of breed-of-origin of alleles. We also applied whole-genome sequencing of ten individuals from a DLY pig family as well as transcriptome of four representative tissues (adipose, skeletal muscle, heart, and liver) for six DLY individuals. Based on above, we identified a large number of high-confidence ASE genes, among which four ASE genes (KMO, PLIN4, POPDC3 and UGT1A6) were found to be shared over all DLY individuals.\n\nConclusionWe suggest DLY is a more effective strategy of three-way crossbreeding among these three purebreds from genetic aspect. We suppose the numerous breed-of-origin of alleles have close association with improved performance of crossbred individuals. ASE may also play important roles on DLY three-way crossbreeding system. Our findings are valuable for understanding the transmission of genetic information and the gene expression in DLY three-way crossbreeding and may be used to guide breeding and production of pigs in the future.

genomics↗

bioRxiv2018

The CIC-DUX4 fusion oncoprotein drives metastasis and tumor growth via distinct downstream regulatory programs and therapeutic targets in sarcoma

Transcription factor fusion genes create oncoproteins that drive oncogenesis, and represent challenging therapeutic targets. Understanding the molecular targets by which such fusion oncoproteins promote malignancy offers an approach to develop rational treatment strategies to improve clinical outcomes. CIC-DUX4 is a transcription factor fusion that defines certain undifferentiated round cell sarcomas with high metastatic propensity and poor clinical outcomes. The molecular targets regulated by the CIC-DUX4 oncoprotein that promote this aggressive malignancy remain largely unknown. We show that increased expression of ETV4 and CCNE1 occurs via neo-morphic, direct effects of CIC-DUX4 and drives tumor metastasis and survival, respectively. We demonstrate a molecular dependence on the CCNE-CDK2 cell cycle complex that renders CIC-DUX4 tumors sensitive to inhibition of the CCNE-CDK2 complex, highlighting a therapeutic strategy for CIC-DUX4 tumors. Our findings highlight a paradigm of functional diversification of transcriptional repertoires controlled by a genetically-aberrant transcriptional regulator, with therapeutic implications.

cancer biology↗

bioRxiv2018

Exploratory study of factors associated with human brucellosis in mainland China based on time-series-cross-section data from 2005 to 2016

ObjectiveMany studies focused on reasons behind the increasing incidence and the spread of human brucellosis in mainland China, yet most of them lacked comprehensive consideration with quantitative evidence. Hence, this study aimed to further investigate the epidemic mechanism and associated factors of human brucellosis in China so as to provide suggestions on more effective countermeasures.\n\nMethodsData of human brucellosis incidence and some associated factors in economy, animal husbandry, transportation and health were collected at provincial level from 2005-2016. Time series plot and cluster analysis were first used to visualize incidence levels and categorize provinces based on their incidence level and epidemic trend of human brucellosis. Furthermore, according to the characteristics of data, the dynamic panel data model in combination with supervised principal component analysis was proposed to explore the effects of associated factors on human brucellosis.\n\nResults[circled1] The incidence rate of human brucellosis has increased threefold (from 1.41 in 2005 to 4.22 in 2016) in mainland China. Incidence rates in the north have always been higher than those in the south, but the latter also experienced an upward trend especially in the recent five years. [circled2] The 31 provinces of mainland China were categorized into three clusters, and each cluster had its own characteristics of incidence level and epidemic trend. [circled3] Public health expenditure and rural medical expenditure proportion were potential protective factors of human brucellosis, with attribute risks of -0.74 and -1.04 respectively. Other factors (such as amount of sheep, total length of highways, etc.) exhibited relatively trivial effects.\n\nConclusionsThe epidemic status of human brucellosis has changed in both spatial and temporal dimensions in recent years. Apart from those traditional control measures, more attention should be paid to the improvement of medical healthcare especially in rural areas in order to strengthen the control effect.

epidemiology↗

bioRxiv2018

A machine learning approach to predicting autism risk genes: Validation of known genes and discovery of new candidates

Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with a strong genetic basis. The role of de novo mutations in ASD has been well established, but the set of genes implicated to date is still far from complete. The current study employs a machine learning-based approach to predict ASD risk genes using features from spatiotemporal gene expression patterns in human brain, gene-level constraint metrics, and other gene variation features. The genes identified through our prediction model were enriched for independent sets of ASD risk genes, and tended to be differentially expressed in ASD brains, especially in the frontal and parietal cortex. The highest-ranked genes not only included those with strong prior evidence for involvement in ASD (for example, TCF20 and FBOX11), but also indicated potentially novel candidates, such as DOCK3, MYCBP2 and CAND1, which are all involved in neuronal development. Through extensive validations, we also showed that our method outperformed state-of-the-art scoring systems for ranking ASD candidate genes. Gene ontology enrichment analysis of our predicted risk genes revealed biological processes clearly relevant to ASD, including neuronal signaling, neurogenesis, and chromatin remodeling, but also highlighted other potential mechanisms that might underlie ASD, such as regulation of RNA alternative splicing and ubiquitination pathway related to protein degradation. Our study demonstrates that human brain spatiotemporal gene expression patterns and gene-level constraint metrics can help predict ASD risk genes. Our gene ranking system provides a useful resource for prioritizing ASD candidate genes.

genetics↗

bioRxiv2018

Integrating brain methylome with GWAS for psychiatric risk gene discovery

DNA methylation (DNAm) is heritable and plays a role in brain development and function through transcriptional regulation. Aberrant DNAm in human brain has been linked to psychiatric disorders, potentially as mediators of common genetic risk variants. In this study, we hypothesize that common risk variants for psychiatric disorders may act through affecting DNAm level in human brain. We first aimed to investigate the heritability pattern of DNAm levels in the human prefrontal cortex. Secondly, through imputation-driven methylome-wide association study (MWAS), we aimed to identify CpG sites whose methylation levels are genetically associated and that show methylation-trait associations in the prefrontal cortex of patients with schizophrenia or bipolar disorder. Our heritability analysis showed that, of ~370,000 CpG sites measured with the Illumina HumanMethylation450 microarray, 17% were heritable (p < 0.05), with a mean heritability of 0.22. Heritable CpG sites were enriched in intergenic regions, CpG shore, and regulatory regions in prefrontal cortex. Our MWAS approach identified known and potentially novel risk genes harboring CpG sites of methylation-trait associations for schizophrenia or bipolar disorder, which were not detectable using three alternative strategies (blood-based methylome reference, transcriptome-wide association study, and two gene-based association tests). Gene set enrichment analysis for genes with methylation-trait association evidence revealed pathways clearly related to neuronal functions, but also highlighted additional biological mechanisms that may underlie psychiatric disorders, such as microRNA-related regulation. In conclusion, our results showed the power of integrating brain methylation data with GWAS for psychiatric risk gene discovery, with potential applications in brain-related disorders or traits.

bioinformatics↗

bioRxiv2018

RegTools: Integrated analysis of genomic and transcriptomic data for discovery of splicing variants in cancer

Somatic mutations within non-coding regions and even exons may have unidentified regulatory consequences that are often overlooked in analysis workflows. Here we present RegTools (www.regtools.org), a computationally efficient, free, and open-source software package designed to integrate somatic variants from genomic data with splice junctions from bulk or single cell transcriptomic data to identify variants that may cause aberrant splicing. RegTools was applied to over 9,000 tumor samples with both tumor DNA and RNA sequence data. We discovered 235,778 events where a splice-associated variant significantly increased the splicing of a particular junction, across 158,200 unique variants and 131,212 unique junctions. To characterize these somatic variants and their associated splice isoforms, we annotated them with the Variant Effect Predictor (VEP), SpliceAI, and Genotype-Tissue Expression (GTEx) junction counts and compared our results to other tools that integrate genomic and transcriptomic data. While many events were corroborated by the aforementioned tools, the flexibility of RegTools also allowed us to identify novel splice-associated variants and previously unreported patterns of splicing disruption in known cancer drivers, such as TP53, CDKN2A, and B2M, as well as in genes not previously considered cancer-relevant.

bioinformatics↗

bioRxiv2018

Narrow equilibrium window for complex coacervation of tau and RNA under cellular conditions

The conditions that lead to the liquid-liquid phase separation (LLPS) of the tau protein, a microtubule associated protein whose pathological aggregation has been implicated in neurodegenerative disorders, are not well understood. Establishing a phase diagram that delineates the boundaries of phase co-existence is key to understanding its LLPS. Using a combination of EPR, turbidity measurements, and microscopy, we show that tau and RNA form complex coacervates with lower critical solution temperature (LCST) behavior. The coacervates are reversible, and the biopolymers can be driven to the supernatant phase or coacervate phase by varying the experimental conditions (temperature, salt concentration, tau:RNA charge ratio, total polymer concentration and osmotic stress). Furthermore, the coacervates can be driven to a fibrillar state through the addition of heparin. The equilibrium phase diagram of the tau/RNA complex coacervate system can be described by a Flory-Huggins model, augmented by an approximate Voorn Overbeek electrostatic term (FH-VO), after fitting the experimental data to an empirical Flory interaction parameter divided into an entropic and enthalpic term. However, a more advanced model in which tau and RNA are treated as discrete bead-spring chains with a temperature-dependent excluded volume interaction and electrostatic interactions between charged residues, investigated through field theoretic simulations (FTS), provided direct and unique insight into the thermodynamic driving forces of tau/RNA complexation. FTS corroborated the experimental finding that the complex coacervation of tau and RNA is has an entropy-driven contribution, with a transition temperature around the physiological temperature of 37 {degrees}C and salt concentrations around 100-150 mM. Together, experiment and simulation show that LLPS of tau can occur under physiological cellular conditions, but has a narrow equilibrium window over experimentally tunable parameters including temperature, salt and tau concentrations. Guided by our phase diagram, we show that tau can be driven towards LLPS under live cell coculturing conditions with rationally chosen experimental parameters.

biophysics↗

bioRxiv2018

Molecular characterization of the viral structural gene of the first dengue virus type 1 outbreak in Xishuangbanna, a border area of China, Burma and Laos

In the context of recent arbovirus epidemics, dengue fever is becoming a greater concern around the world. In August 2017, Xishuangbanna, which is a border city of China, Burma and Laos, had its first major dengue outbreak. A total of 156 serum samples from febrile patients were collected; 97 DENV positive serum samples were screened out, and viral RNAs were successfully and directly extracted, including 77 cases from China and 20 cases from Myanmar. Phylogenetic analysis revealed that all of the strains were classified as DENV-1. There are eight epidemic dengue strains from Myanmar and 74 from Jinghong, Xishuangbanna, that were classified as cluster 1, which are the most similar to the strain of China Guangzhou 2011. There are three epidemic strains from Xishuangbanna Mengla that were classified as cluster 2, which have the closest relationship to the strain of China Hubei 2014. However, there are 12 epidemic strains from Myanmar that were classified as cluster 3, which have the closest relationship to the strain of Laos from 2008, which shows that there is a recycling epidemic trend of DENV in China. There were 236 mutations in the base, which caused 31 nonsynonymous mutations in the DENV structural protein C/prM/E genes when the strain of Xishuangbanna and Myanmar were compared with the DENV-1SS. There is no clear homologous recombination signal among these stains. Homology modeling possibly predicted a three-dimensional structure of the structural protein of these strains and revealed that they had the same three-dimensional structure and all had five predicted protein binding sites, but there are differences in binding site 434 (DENV-1SS: Thr434, DV-Jinghong: Ser434, DV-Myanmar: Ser434, DV-Mengla: Ser434). The results of the molecular clock phylogenetic and demographic reconstruction analysis show that DENV-1 became highly diversified in 1972 followed by a slightly decreased period until 2017. In conclusion, our study lays the foundation for studying the global evolution and prevalence of DENV.\n\nAuthor SummaryDengue fever (DF) is a mosquito-borne illness caused by a flavivirus. Human infections with Dengue virus (DENV) could cause fever, cutaneous rash and malaise. Xishuangbanna, which is located in the southwestern Yunnan Province and is a border city with China, Burma and Laos, was reported to have outbreak of DENV in 2013 and 2015 with different types. However, there was a large outburst of dengue in May 2017. To understand the genetic characterization, potential source and evolution of the virus, 156 serum samples were analyzed. We focused on: (i) Phylogenetic analysis of the structural protein genes sequences; (ii) Mutation, recombination analysis and predicted protein binding sites of the structural protein genes; (iii) Molecular clock and demographic reconstruction of global dengue virus serotype 1(DENV-1). Our results indicated that this is the first outbreak of DENV-1 in Xishuangbanna, dengue epidemic strains on the Burma border of China show diversification, we found a virulence site changed from I to T(amino acid position: 440), which may lead to weakened virulence of the epidemic strains. We found that the evolution of DENV-1 is dominated by regional evolution. Whats more, DENV-1 became highly diversified in 1972 followed by a slightly decreased period until 2017.

epidemiology↗

bioRxiv2018

Profile of the tprK gene in primary syphilis patients based on next-generation sequencing

BackgroundThe highly variable tprK gene of Treponema pallidum has been acknowledged to be the cause of persistent infection. Previous studies mainly focused on the heterogeneity in tprK in propagated strains using a clone-based Sanger approach. Few studies have investigated tprK directly from clinical samples using deep sequencing.\n\nMethods/Principal findingsWe conducted a comprehensive analysis of 14 primary syphilis clinical isolates of T. pallidum via next-generation sequencing to gain better insight into the profile of tprK in primary syphilis patients. Our results based on primary syphilis clinical samples showed that there was a mixture of distinct sequences within each V region of tprK. Except for the predominant sequence for each region as previously reported using the clone-based Sanger approach, there were many minor variants of all strains that were mainly observed at a frequency of 1-5%. Interestingly, the identified distinct sequences within the regions were variable in length and differed only by 3 bp or multiples of 3 bp. In addition, amino acid sequence consistency within each region was found between the 14 strains. Among the regions, the sequence IASDGGAIKH in V1 and the sequence DVGHKKENAANVNGTVGA in V4 showed a high stability of inter-strain redundancy.\n\nConclusionsThe seven V regions of the tprK gene in primary syphilis infection demonstrated high diversity; they generally contained a high proportion sequence and numerous low-frequency minor variants, most of which are far below the detection limit of Sanger sequencing. The rampant variation in each region was regulated by a strict gene conversion mechanism that maintained the length difference to 3 bp or multiples of 3 bp. The highly stable sequence of inter-strain redundancy may indicate that the sequences play a critical role in T. pallidum virulence. These highly stable peptides are also likely to be potential targets for vaccine development.\n\nAuthor summaryVariations in tprK have been acknowledged to be the major contributors to persistent Treponema pallidum infections. Previous studies were based on the clone-based Sanger approach, and most of them were performed in propagated strains using rabbits, which could not reflect the actual heterogeneous characteristics of tprK in vivo. In the present study, we employed next-generation sequencing (NGS) to explore the profile of tprK directly from 14 patients with primary syphilis. Our results showed a mixture of distinct sequences within each V region of tprK in these clinical samples. First, the length of identified distinct sequences within the region was variable, which differed by only 3 bp or multiples of 3 bp. Then, among the mixtures, a predominant sequence was usually observed for each region, and the remaining minor variants were mainly observed at a frequency of 1-5%. In addition, there was a scenario of amino acid sequence consistency within the regions between the 14 primary syphilis strains. The identification of the profile of tprK in the context of human primary syphilis infection contributes to further exploration of the pathogenesis of syphilis.

microbiology↗

bioRxiv2018

Zinc Boosts EGCG’s hIAPP Amyloid Inhibition Both in Solution and Membrane

Amyloid aggregation of human islet amyloid polypeptide (hIAPP) is linked to insulin-producing islet cell death in type II diabetes. Previous studies have shown the amyloid inhibiting effects of zinc (Zn) and insulin that are co-present with hIAPP in islet cells, and the lipid membrane has been shown to significantly influence the aggregation kinetics. Increasing number of studies report the importance of developing small molecule inhibitors to suppress the hIAPPs toxicity. Particularly, the ability of epigallocatechin-gallate (EGCG) to inhibit amyloid aggregation of a variety of amyloid peptide/proteins including hIAPP initiated numerous studies including the development of compounds to potentially treat amyloid diseases. In this study, by using a combination of thioflavin-T fluorescence and transmission electron microscopy experiments, we demonstrate a significant enhancement in EGCGs efficiency, when mixed with Zn, to significantly suppress hIAPP amyloid aggregation both in presence and absence of lipid membrane. Circular dichroism experiments indicate the formation and stabilization of a helical structure of hIAPP in presence of EGCG:Zn complex. Our results also reveal the ability of EGCG or EGCG:Zn to suppress hIAPPs cellular toxicity and that the ability of EGCG to chelate with Zn suppresses zincs cellular toxicity. We suggest that the reported results would be useful to develop strategies to trap hIAPP intermediates for further biophysical and structural studies, and also to devise approaches to abolish amyloid aggregation and cellular toxicity.

biophysics↗

bioRxiv2018

scMerge: Integration of multiple single-cell transcriptomics datasets leveraging stable expression and pseudo-replication

Concerted examination of multiple collections of single cell RNA-Seq (scRNA-Seq) data promises further biological insights that cannot be uncovered with individual datasets. However, such integrative analyses are challenging and require sophisticated methodologies. To enable effective interrogation of multiple scRNA-Seq datasets, we have developed a novel algorithm, named scMerge, that removes unwanted variation by combining stably expressed genes and utilizing pseudo-replicates across datasets. Analysis of large collections of publicly available datasets demonstrates that scMerge performs well in multiple scenarios and enhances biological discovery, including inferring cell developmental trajectories.

bioinformatics↗